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Microorganisms, Volume 10, Issue 8 (August 2022) – 208 articles

Cover Story (view full-size image): Chronic wounds, which respond poorly to treatment, are a major concern worldwide, affecting millions of patients every year. The microorganisms colonising the wound contribute to the establishment of chronicity through polymicrobial biofilm. Clinical management of chronic wounds relies on tissue debridement at regular intervals, which removes dead tissue, and the associated microbial communities, contributing to reorganize them. The complex network of species and interactions found in chronic wounds has the potential, through antagonist and/or synergistic crosstalk between different microorganisms, to accelerate or to impair wound healing. Understanding these interactions between microorganisms encountered in this clinical situation is essential to improve the management of chronic wounds. View this paper
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15 pages, 2293 KiB  
Article
Loss of rpoE Encoding the δ-Factor of RNA Polymerase Impacts Pathophysiology of the Streptococcus pyogenes M1T1 Strain 5448
by Joseph S. Rom, Yoann Le Breton, Emrul Islam, Ashton T. Belew, Najib M. El-Sayed and Kevin S. McIver
Microorganisms 2022, 10(8), 1686; https://doi.org/10.3390/microorganisms10081686 - 22 Aug 2022
Cited by 1 | Viewed by 1551
Abstract
Streptococcus pyogenes, also known as the Group A Streptococcus (GAS), is a Gram-positive bacterial pathogen of major clinical significance. Despite remaining relatively susceptible to conventional antimicrobial therapeutics, GAS still causes millions of infections and hundreds of thousands of deaths each year worldwide. [...] Read more.
Streptococcus pyogenes, also known as the Group A Streptococcus (GAS), is a Gram-positive bacterial pathogen of major clinical significance. Despite remaining relatively susceptible to conventional antimicrobial therapeutics, GAS still causes millions of infections and hundreds of thousands of deaths each year worldwide. Thus, a need for prophylactic and therapeutic interventions for GAS is in great demand. In this study, we investigated the importance of the gene encoding the delta (δ) subunit of the GAS RNA polymerase, rpoE, for its impact on virulence during skin and soft-tissue infection. A defined 5448 mutant with an insertionally-inactivated rpoE gene was defective for survival in whole human blood and was attenuated for both disseminated lethality and lesion size upon mono-culture infection in mouse soft tissue. Furthermore, the mutant had reduced competitive fitness when co-infected with wild type (WT) 5448 in the mouse model. We were unable to attribute this attenuation to any observable growth defect, although colony size and the ability to grow at higher temperatures were both affected when grown with nutrient-rich THY media. RNA-seq of GAS grown in THY to late log phase found that mutation of rpoE significantly impacted (>2-fold) the expression of 429 total genes (205 upregulated, 224 downregulated), including multiple virulence and “housekeeping” genes. The arc operon encoding the arginine deiminase (ADI) pathway was the most upregulated in the rpoE mutant and this could be confirmed phenotypically. Taken together, these findings demonstrate that the delta (δ) subunit of RNA polymerase is vital in GAS gene expression and virulence. Full article
(This article belongs to the Special Issue Pathogenic Streptococci: Virulence, Host Response and Therapy)
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15 pages, 1059 KiB  
Article
Herpesvirus Screening in Childhood Hematopoietic Transplant Reveals High Systemic Inflammation in Episodes of Multiple Viral Detection and an EBV Association with Elevated IL-1β, IL-8 and Graft-Versus-Host Disease
by Moisés H. Rojas-Rechy, Félix Gaytán-Morales, Yessica Sánchez-Ponce, Iván Castorena-Villa, Briceida López-Martínez, Israel Parra-Ortega, María C. Escamilla-Núñez, Alfonso Méndez-Tenorio, Ericka N. Pompa-Mera, Gustavo U. Martinez-Ruiz, Ezequiel M. Fuentes-Pananá and Abigail Morales-Sánchez
Microorganisms 2022, 10(8), 1685; https://doi.org/10.3390/microorganisms10081685 - 22 Aug 2022
Cited by 3 | Viewed by 2013
Abstract
Infections remain a major cause of morbidity and mortality among hematopoietic stem cell transplant (HSCT) recipients. Unlike Epstein–Barr Virus (EBV) and Human Cytomegalovirus (HCMV), Human Herpesvirus (HHV) 6, HHV7 and HHV8 are not routinely monitored in many centers, especially in the pediatric population [...] Read more.
Infections remain a major cause of morbidity and mortality among hematopoietic stem cell transplant (HSCT) recipients. Unlike Epstein–Barr Virus (EBV) and Human Cytomegalovirus (HCMV), Human Herpesvirus (HHV) 6, HHV7 and HHV8 are not routinely monitored in many centers, especially in the pediatric population of low–medium income countries. We screened EBV, HCMV, HHV6, HHV7 and HHV8 in 412 leukocytes-plasma paired samples from 40 pediatric patients assisted in a tertiary hospital in Mexico. Thirty-two underwent allo-HSCT, whereas eight received auto-HSCT. Overall viral detection frequencies in allo- and auto-HSCT were: EBV = 43.7% and 30.0%, HCMV = 5.0% and 6.7%, HHV6 = 7.9% and 20.0% and HHV7 = 9.7% and 23.3%. HHV8 was not detected in any sample. Interestingly, HHV6 and HHV7 were more frequent in auto-HSCT, and HHV6 was observed in all episodes of multiple detection in auto-HSCT patients. We found EBV DNA in plasma samples, whereas HCMV, HHV6 and HHV7 DNA were predominantly observed in leukocytes, indicative of their expansion in cellular compartments. We also found that IL-1β, IL-2, IL-6 and IL-8 were significantly increased in episodes in which multiple viruses were simultaneously detected, and samples positive for EBV DNA and graft-versus-host disease had a further increase of IL-1β and IL-8. In conclusion, the EBV, HCMV, HHV6 and HHV7 burdens were frequently detected in allo- and auto-HSCT, and their presence associated with systemic inflammation. Full article
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17 pages, 918 KiB  
Article
Evidence of Community-Wide Spread of Multi-Drug Resistant Escherichia coli in Young Children in Lusaka and Ndola Districts, Zambia
by Flavien Nsoni Bumbangi, Ann-Katrin Llarena, Eystein Skjerve, Bernard Mudenda Hang’ombe, Prudence Mpundu, Steward Mudenda, Paulin Beya Mutombo and John Bwalya Muma
Microorganisms 2022, 10(8), 1684; https://doi.org/10.3390/microorganisms10081684 - 21 Aug 2022
Cited by 9 | Viewed by 2177
Abstract
Increased antimicrobial resistance (AMR) has been reported for pathogenic and commensal Escherichia coli (E. coli), hampering the treatment, and increasing the burden of infectious diarrhoeal diseases in children in developing countries. This study focused on exploring the occurrence, patterns, and possible drivers [...] Read more.
Increased antimicrobial resistance (AMR) has been reported for pathogenic and commensal Escherichia coli (E. coli), hampering the treatment, and increasing the burden of infectious diarrhoeal diseases in children in developing countries. This study focused on exploring the occurrence, patterns, and possible drivers of AMR E. coli isolated from children under-five years in Zambia. A hospital-based cross-sectional study was conducted in the Lusaka and Ndola districts. Rectal swabs were collected from 565 and 455 diarrhoeic and healthy children, respectively, from which 1020 E. coli were cultured and subjected to antibiotic susceptibility testing. Nearly all E. coli (96.9%) were resistant to at least one antimicrobial agent tested. Further, 700 isolates were Multi-Drug Resistant, 136 were possibly Extensively-Drug Resistant and nine were Pan-Drug-Resistant. Forty percent of the isolates were imipenem-resistant, mostly from healthy children. A questionnaire survey documented a complex pattern of associations between and within the subgroups of the levels of MDR and socio-demographic characteristics, antibiotic stewardship, and guardians’ knowledge of AMR. This study has revealed the severity of AMR in children and the need for a community-specific-risk-based approach to implementing measures to curb the problem. Full article
(This article belongs to the Special Issue Clinical Microbiology and Antimicrobial Stewardship)
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12 pages, 1755 KiB  
Article
The Gene Expression Profile Differs in Growth Phases of the Bifidobacterium Longum Culture
by Vladimir A. Veselovsky, Marina S. Dyachkova, Dmitry A. Bespiatykh, Roman A. Yunes, Egor A. Shitikov, Polina S. Polyaeva, Valeriy N. Danilenko, Evgenii I. Olekhnovich and Ksenia M. Klimina
Microorganisms 2022, 10(8), 1683; https://doi.org/10.3390/microorganisms10081683 - 21 Aug 2022
Cited by 8 | Viewed by 2002
Abstract
To date, transcriptomics have been widely and successfully employed to study gene expression in different cell growth phases of bacteria. Since bifidobacteria represent a major component of the gut microbiota of a healthy human that is associated with numerous health benefits for the [...] Read more.
To date, transcriptomics have been widely and successfully employed to study gene expression in different cell growth phases of bacteria. Since bifidobacteria represent a major component of the gut microbiota of a healthy human that is associated with numerous health benefits for the host, it is important to study them using transcriptomics. In this study, we applied the RNA-Seq technique to study global gene expression of B. longum at different growth phases in order to better understand the response of bifidobacterial cells to the specific conditions of the human gut. We have shown that in the lag phase, ABC transporters, whose function may be linked to active substrate utilization, are increasingly expressed due to preparation for cell division. In the exponential phase, the functions of activated genes include synthesis of amino acids (alanine and arginine), energy metabolism (glycolysis/gluconeogenesis and nitrogen metabolism), and translation, all of which promote active cell division, leading to exponential growth of the culture. In the stationary phase, we observed a decrease in the expression of genes involved in the control of the rate of cell division and an increase in the expression of genes involved in defense-related metabolic pathways. We surmise that the latter ensures cell survival in the nutrient-deprived conditions of the stationary growth phase. Full article
(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)
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18 pages, 2703 KiB  
Article
Antifungal Activity and Plant Growth-Promoting Properties of Bacillus mojovensis B1302 against Rhizoctonia Cerealis
by Yanjie Yi, Pengyu Luan, Kang Wang, Guiling Li, Yanan Yin, Yanhui Yang, Qingyao Zhang and Yang Liu
Microorganisms 2022, 10(8), 1682; https://doi.org/10.3390/microorganisms10081682 - 20 Aug 2022
Cited by 8 | Viewed by 2156
Abstract
Rhizoctonia cerealis is a worldwide soil-borne pathogenic fungus that significantly infects wheat and causes sharp eyespot in China. However, the biocontrol strains used for the control of Rhizoctonia cerealis are insufficient. In the present study, antagonistic strain B1302 from the rhizosphere of wheat [...] Read more.
Rhizoctonia cerealis is a worldwide soil-borne pathogenic fungus that significantly infects wheat and causes sharp eyespot in China. However, the biocontrol strains used for the control of Rhizoctonia cerealis are insufficient. In the present study, antagonistic strain B1302 from the rhizosphere of wheat were isolated and identified as Bacillus mojovensis based on their morphological, physiological, and biochemical characteristics, and their 16S rDNA sequence. Culture filtrate of strain B1302 had a broad antifungal spectrum. In order to improve the antifungal activity of B1302, response surface methodology (RSM) was used to optimize the culture conditions. The final medium composition and culture conditions were 13.2 g/L of wheat bran, 14.1 g/L of soybean meal, 224 r/min of rotation speed, 7.50 of initial pH, and 1.5 × 108 CFU/mL of inoculation amount at 35 °C for a culture duration of 72 h. B. mojavensis B1302 inhibited the hyphae growth of R.cerealis and produced hydrolytic enzymes (protease, chitinase, and glucanase), IAA, and had N-fixing potentiality and P-solubilisation capacity. It can also promote wheat seedling growth in potted plants. The disease incidence and index of wheat seedlings were consistent with the effect of commercial pesticides under treatment with culture filtrate. The biocontrol efficacy of culture filtrate was significant—up to 65.25%. An animal toxicological safety analysis suggested that culture filtrate was safe for use and could be developed into an effective microbial fungicide to control wheat sharp eyespot. Full article
(This article belongs to the Special Issue Antifungal Activity of Bacillus Species against Plant Pathogens)
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7 pages, 658 KiB  
Communication
Phylogenomic Placement of American Southwest-Associated Clinical and Veterinary Isolates Expands Evidence for Distinct Cryptococcus gattii VGVI
by Juan Monroy-Nieto, Jolene R. Bowers, Parker Montfort, Guillermo Adame, Constanza Giselle Taverna, Hayley Yaglom, Jane E. Sykes, Shane Brady, A. Brian Mochon, Wieland Meyer, Kenneth Komatsu and David M. Engelthaler
Microorganisms 2022, 10(8), 1681; https://doi.org/10.3390/microorganisms10081681 - 20 Aug 2022
Cited by 4 | Viewed by 1668
Abstract
Whole-genome sequencing has advanced our understanding of the population structure of the pathogenic species complex Cryptococcus gattii, which has allowed for the phylogenomic specification of previously described major molecular type groupings and novel lineages. Recently, isolates collected in Mexico in the [...] Read more.
Whole-genome sequencing has advanced our understanding of the population structure of the pathogenic species complex Cryptococcus gattii, which has allowed for the phylogenomic specification of previously described major molecular type groupings and novel lineages. Recently, isolates collected in Mexico in the 1960s were determined to be genetically distant from other known molecular types and were classified as VGVI. We sequenced four clinical isolates and one veterinary isolate collected in the southwestern United States and Argentina from 2012 to 2021. Phylogenomic analysis groups these genomes with those of the Mexican VGVI isolates, expanding VGVI into a clade and establishing this molecular type as a clinically important population. These findings also potentially expand the known Cryptococcus ecological range with a previously unrecognized endemic area. Full article
(This article belongs to the Special Issue Advances in Cryptococcus and Cryptococcosis)
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20 pages, 4445 KiB  
Article
Effects of Light on Growth and Metabolism of Rhodococcus erythropolis
by Selina Engelhart-Straub, Philipp Cavelius, Fabian Hölzl, Martina Haack, Dania Awad, Thomas Brueck and Norbert Mehlmer
Microorganisms 2022, 10(8), 1680; https://doi.org/10.3390/microorganisms10081680 - 20 Aug 2022
Cited by 8 | Viewed by 2230
Abstract
Rhodococcus erythropolis is resilient to various stressors. However, the response of R. erythropolis towards light has not been evaluated. In this study, R. erythropolis was exposed to different wavelengths of light. Compared to non-illuminated controls, carotenoid levels were significantly increased in white (standard [...] Read more.
Rhodococcus erythropolis is resilient to various stressors. However, the response of R. erythropolis towards light has not been evaluated. In this study, R. erythropolis was exposed to different wavelengths of light. Compared to non-illuminated controls, carotenoid levels were significantly increased in white (standard warm white), green (510 nm) and blue light (470 nm) illuminated cultures. Notably, blue light (455, 425 nm) exhibited anti-microbial effects. Interestingly, cellular lipid composition shifted under light stress, increasing odd chain fatty acids (C15:0, C17:1) cultured under white (standard warm white) and green (510 nm) light. When exposed to blue light (470, 455, 425 nm), fatty acid profiles shifted to more saturated fatty acids (C16:1 to C16:0). Time-resolved proteomics analysis revealed several oxidative stress-related proteins to be upregulated under light illumination. Full article
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19 pages, 596 KiB  
Review
Virulence Characteristics and Distribution of the Pathogen Listeria ivanovii in the Environment and in Food
by Franca Rossi, Valerio Giaccone, Giampaolo Colavita, Carmela Amadoro, Francesco Pomilio and Paolo Catellani
Microorganisms 2022, 10(8), 1679; https://doi.org/10.3390/microorganisms10081679 - 20 Aug 2022
Cited by 2 | Viewed by 2108
Abstract
Listeria ivanovii and L. monocytogenes, are the only pathogenic species of the genus Listeria and share many virulence factors and mechanisms of pathogenicity. L. ivanovii shows host tropism towards small ruminants and rodents and much lower virulence for humans compared to L. [...] Read more.
Listeria ivanovii and L. monocytogenes, are the only pathogenic species of the genus Listeria and share many virulence factors and mechanisms of pathogenicity. L. ivanovii shows host tropism towards small ruminants and rodents and much lower virulence for humans compared to L. monocytogenes. However, severe infections caused by L. ivanovii, resulting in bacteremia, abortion and stillbirth, occasionally occurred in immunocompromised persons and in pregnant women, while in immunocompetent hosts L. ivanovii can cause gastroenteritis. In this review, the updated knowledge on virulence aspects and distribution of L. ivanovii in the environment and in food is summarized. Recent research on its virulence characters at genome level gave indications on how pathogenicity evolved in this bacterial species. As for L. monocytogenes, L. ivanovii infections occurred after the ingestion of contaminated food, so an overview of reports regarding its distribution in food products was carried out to obtain indications on the categories of foods exposed to contamination by L. ivanovii. It was found that a wide variety of food products can be a source of this microorganism and that, like L. monocytogenes, L. ivanovii is able to persist in the food production environment. Studies on its ability to grow in enrichment and isolation media suggested that its occurrence in nature might be underestimated. Moreover, virulence varies among strains for differences in virulence character regulation, presence/absence of genetic regions and the possible instability of a Listeria pathogenicity genomic island, LIPI-2, which is unique to L. ivanovii. We can conclude that L. ivanovii, as a possible pathogen for animals and humans, requires more focused investigations regarding its occurrence in the environment and in food and on intra-species variability of pathogenic potential. Full article
(This article belongs to the Section Food Microbiology)
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2 pages, 166 KiB  
Editorial
Plasmids Carrying Antimicrobial Resistance Genes in Gram-Negative Bacteria
by Nadezhda K. Fursova, Angelina A. Kislichkina and Olga E. Khokhlova
Microorganisms 2022, 10(8), 1678; https://doi.org/10.3390/microorganisms10081678 - 20 Aug 2022
Cited by 6 | Viewed by 1278
Abstract
Gram-negative bacteria are prevalent pathogens associated with hospital-acquired infections (HAI) that are a major challenge for patient safety, especially in intensive care units [...] Full article
(This article belongs to the Special Issue Antimicrobial Resistance Mechanisms in Bacteria)
13 pages, 2392 KiB  
Article
Insights into the Bacterial Diversity and Detection of Opportunistic Pathogens in Mexican Chili Powder
by Yoali Fernanda Hernández Gómez, Jacqueline González Espinosa, Miguel Ángel Ramos López, Jackeline Lizzeta Arvizu Gómez, Carlos Saldaña, José Alberto Rodríguez Morales, María Carlota García Gutiérrez, Victor Pérez Moreno, Erika Álvarez Hidalgo, Jorge Nuñez Ramírez, George H. Jones, José Luis Hernández Flores and Juan Campos Guillén
Microorganisms 2022, 10(8), 1677; https://doi.org/10.3390/microorganisms10081677 - 20 Aug 2022
Cited by 4 | Viewed by 2456
Abstract
Chili powder is the most frequently consumed spice in Mexican diets. Thus, the dissemination of microorganisms associated with chili powder derived from Capsicum annuum L. is significant during microbial quality analysis, with special attention on detection of potential pathogens. The results presented here [...] Read more.
Chili powder is the most frequently consumed spice in Mexican diets. Thus, the dissemination of microorganisms associated with chili powder derived from Capsicum annuum L. is significant during microbial quality analysis, with special attention on detection of potential pathogens. The results presented here describe the initial characterization of bacterial community structure in commercial chili powder samples. Our results demonstrate that, within the domain Bacteria, the most abundant family was Bacillaceae, with a relative abundance of 99% in 71.4% of chili powder samples, while 28.6% of samples showed an average relative abundance of 60% for the Enterobacteriaceae family. Bacterial load for aerobic mesophilic bacteria (AMB) ranged from 104 to 106 cfu/g, while for sporulated mesophilic bacteria (SMB), the count ranged from 102 to 105 cfu/g. Bacillus cereus sensu lato (s.l.) was observed at ca. ˂600 cfu/g, while the count for Enterobacteriaceae ranged from 103 to 106 cfu/g, Escherichia coli and Salmonella were not detected. Fungal and yeast counts ranged from 102 to 105 cfu/g. Further analysis of the opportunistic pathogens isolated, such as B. cereus s.l. and Kosakonia cowanii, using antibiotic-resistance profiles and toxinogenic characteristics, revealed the presence of extended-spectrum β-lactamases (ESBLs) and Metallo-β-lactamases (MBLs) in these organisms. These results extend our knowledge of bacterial diversity and the presence of opportunistic pathogens associated with Mexican chili powder and highlight the potential health risks posed by its use through the spread of antibiotic-resistance and the production of various toxins. Our findings may be useful in developing procedures for microbial control during chili powder production. Full article
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14 pages, 1955 KiB  
Article
Uninvited Guest: Arrival and Dissemination of Omicron Lineage SARS-CoV-2 in St. Petersburg, Russia
by Anna Gladkikh, Vladimir Dedkov, Alena Sharova, Ekaterina Klyuchnikova, Valeriya Sbarzaglia, Tatiana Arbuzova, Majid Forghani, Edward Ramsay, Anna Dolgova, Anna Shabalina, Nadezhda Tsyganova and Areg Totolian
Microorganisms 2022, 10(8), 1676; https://doi.org/10.3390/microorganisms10081676 - 20 Aug 2022
Cited by 4 | Viewed by 1775
Abstract
Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze [...] Read more.
Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia’s second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
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18 pages, 12396 KiB  
Article
Fungal Lignocellulose Utilisation Strategies from a Bioenergetic Perspective: Quantification of Related Functional Traits Using Biocalorimetry
by Hieu Linh Duong, Sven Paufler, Hauke Harms, Dietmar Schlosser and Thomas Maskow
Microorganisms 2022, 10(8), 1675; https://doi.org/10.3390/microorganisms10081675 - 19 Aug 2022
Cited by 2 | Viewed by 1469
Abstract
In the present study, we investigated whether a non-invasive metabolic heat flux analysis could serve the determination of the functional traits in free-living saprotrophic decomposer fungi and aid the prediction of fungal influences on ecosystem processes. For this, seven fungi, including ascomycete, basidiomycete, [...] Read more.
In the present study, we investigated whether a non-invasive metabolic heat flux analysis could serve the determination of the functional traits in free-living saprotrophic decomposer fungi and aid the prediction of fungal influences on ecosystem processes. For this, seven fungi, including ascomycete, basidiomycete, and zygomycete species, were investigated in a standardised laboratory environment, employing wheat straw as a globally relevant lignocellulosic substrate. Our study demonstrates that biocalorimetry can be employed successfully to determine growth-related fungal activity parameters, such as apparent maximum growth rates (AMGR), cultivation times until the observable onset of fungal growth at AMGR (tAMGR), quotients formed from the AMGR and tAMGR (herein referred to as competitive growth potential, CGP), and heat yield coefficients (YQ/X), the latter indicating the degree of resource investment into fungal biomass versus other functional attributes. These parameters seem suitable to link fungal potentials for biomass production to corresponding ecological strategies employed during resource utilisation, and therefore may be considered as fungal life history traits. A close connection exists between the CGP and YQ/X values, which suggests an interpretation that relates to fungal life history strategies. Full article
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8 pages, 3355 KiB  
Article
Phage vB_YenS_P400, a Novel Virulent Siphovirus of Yersinia enterocolitica Isolated from Deer
by Jens A. Hammerl, Andrea Barac, Claudia Jäckel, Julius Fuhrmann, Ashish Gadicherla and Stefan Hertwig
Microorganisms 2022, 10(8), 1674; https://doi.org/10.3390/microorganisms10081674 - 19 Aug 2022
Cited by 1 | Viewed by 1265
Abstract
Phage vB_YenS_P400 isolated from deer, is a virulent siphovirus of Y. enterocolitica, whose circularly permutated genome (46,585 bp) is not substantially related to any other phage deposited in public nucleotide databases. vB_YenS_P400 showed a very narrow host range and exclusively lysed two [...] Read more.
Phage vB_YenS_P400 isolated from deer, is a virulent siphovirus of Y. enterocolitica, whose circularly permutated genome (46,585 bp) is not substantially related to any other phage deposited in public nucleotide databases. vB_YenS_P400 showed a very narrow host range and exclusively lysed two Y. enterocolitica B4/O:3 strains. Moreover, lytic activity by this phage was only discernible at room temperature. Together with the finding that vB_YenS_P400 revealed a long latent period (90 to 100 min) and low burst size (five to ten), it is not suitable for applications but provides insight into the diversity of Yersinia phages. Full article
(This article belongs to the Section Virology)
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20 pages, 1761 KiB  
Article
Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment
by Júnia Schultz, Mariana Teixeira Dornelles Parise, Doglas Parise, Laenne G. Medeiros, Thiago J. Sousa, Rodrigo B. Kato, Ana Paula Trovatti Uetanabaro, Fabrício Araújo, Rommel Thiago Jucá Ramos, Siomar de Castro Soares, Bertram Brenig, Vasco Ariston de Carvalho Azevedo, Aristóteles Góes-Neto and Alexandre S. Rosado
Microorganisms 2022, 10(8), 1673; https://doi.org/10.3390/microorganisms10081673 - 19 Aug 2022
Cited by 2 | Viewed by 3079
Abstract
Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in [...] Read more.
Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments. However, the phylogeny of this genus and its adaptive mechanisms in the geothermal sites of cold environments remain unknown. To the best of our knowledge, this is the first study to unravel the genomic features and provide insights into the phylogenomics and metabolic potential of members of the genus Anoxybacillus inhabiting the Antarctic thermophilic ecosystem. Here, we report the genome sequencing data of seven A. flavithermus strains isolated from two geothermal sites on Deception Island, Antarctic Peninsula. Their genomes were approximately 3.0 Mb in size, had a G + C ratio of 42%, and were predicted to encode 3500 proteins on average. We observed that the strains were phylogenomically closest to each other (Average Nucleotide Identity (ANI) > 98%) and to A. flavithermus (ANI 95%). In silico genomic analysis revealed 15 resistance and metabolic islands, as well as genes related to genome stabilization, DNA repair systems against UV radiation threats, temperature adaptation, heat- and cold-shock proteins (Csps), and resistance to alkaline conditions. Remarkably, glycosyl hydrolase enzyme-encoding genes, secondary metabolites, and prophage sequences were predicted, revealing metabolic and cellular capabilities for potential biotechnological applications. Full article
(This article belongs to the Special Issue Microbial Adaptations and Genomes under Extreme Conditions)
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16 pages, 4486 KiB  
Article
The Association between Gut Microbiome Diversity and Composition and Heat Tolerance in Cattle
by Xiaohui Zhang, Ke Cui, Xiaobo Wen, Lianbin Li, Xiangchun Yu, Boling Li, Haichao Lin, Hongxuan He and Fengyang Wang
Microorganisms 2022, 10(8), 1672; https://doi.org/10.3390/microorganisms10081672 - 19 Aug 2022
Cited by 3 | Viewed by 1797
Abstract
Cattle are raised around the world and are frequently exposed to heat stress, whether in tropical countries or in regions with temperate climates. It is universally acknowledged that compared to those in temperate areas, the cattle breeds developed in tropical and subtropical areas [...] Read more.
Cattle are raised around the world and are frequently exposed to heat stress, whether in tropical countries or in regions with temperate climates. It is universally acknowledged that compared to those in temperate areas, the cattle breeds developed in tropical and subtropical areas have better heat tolerance. However, the underlying mechanism of heat tolerance has not been fully studied, especially from the perspective of intestinal microbiomics. The present study collected fecal samples of cattle from four representative climatic regions of China, namely, the mesotemperate (HLJ), warm temperate (SD), subtropical (HK), and tropical (SS) regions. Then, the feces were analyzed using high-throughput 16S rRNA sequencing. The results showed that with increasing climatic temperature from HLJ to SS, the abundance of Firmicutes increased, accompanied by an increasing Firmicutes to Bacteroidota ratio. Proteobacteria showed a trend of reduction from HLJ to SS. Patescibacteria, Chloroflexi, and Actinobacteriota were particularly highest in SS for adapting to the tropical environment. The microbial phenotype in the tropics was characterized by an increase in Gram-positive bacteria and a decrease in Gram-negative bacteria, aerobic bacteria, and the forming of_biofilms. Consistently, the functional abundances of organismal systems and metabolism were decreased to reduce the material and energy demands in a hot environment. Genetic information processing and information storage and processing may be how gut flora deals with hot conditions. The present study revealed the differences in the structure and function of gut microbes of cattle from mesotemperate to tropical climates and provided an important reference for future research on the mechanism of heat tolerance regulated by the gut microbiota and a potential microbiota-based target to alleviate heat stress. Full article
(This article belongs to the Section Gut Microbiota)
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13 pages, 601 KiB  
Review
How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research
by Laura K. Inglis and Robert A. Edwards
Microorganisms 2022, 10(8), 1671; https://doi.org/10.3390/microorganisms10081671 - 19 Aug 2022
Cited by 7 | Viewed by 2492
Abstract
The microbiome is an essential part of most ecosystems. It was originally studied mostly through culturing but relatively few microbes can be cultured, so much of the microbiome was left unexplored. The emergence of metagenomic sequencing techniques changed that and allowed the study [...] Read more.
The microbiome is an essential part of most ecosystems. It was originally studied mostly through culturing but relatively few microbes can be cultured, so much of the microbiome was left unexplored. The emergence of metagenomic sequencing techniques changed that and allowed the study of microbiomes from all sorts of habitats. Metagenomic sequencing also allowed for a more thorough exploration of prophages, viruses that integrate into bacterial genomes, and how they benefit their hosts. One issue with using open-access metagenomic data is that sequences added to databases often have little to no metadata to work with, so finding enough sequences can be difficult. Many metagenomes have been manually curated but this is a time-consuming process and relies heavily on the uploader to be accurate and thorough when filling in metadata fields and the curators to be working with the same ontologies. Using algorithms to automatically sort metagenomes based on either the taxonomic profile or the functional profile may be a viable solution to the issues with manually curated metagenomes, but it requires that the algorithm is trained on carefully curated datasets and using the most informative profile possible in order to minimize errors. Full article
(This article belongs to the Section Systems Microbiology)
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19 pages, 1533 KiB  
Article
Bioactives and Extracellular Enzymes Obtained from Fermented Macrofungi Cultivated in Cotton and Jatropha Seed Cakes
by Joice Raísa Barbosa Cunha, Daiana Wischral, Ruben Darío Romero Pelaez, Maria Aparecida de Jesus, Ceci Sales-Campos, Raquel Bombarda Campanha, Thais Demarchi Mendes, Simone Mendonça, Eustáquio Souza Dias and Félix Gonçalves de Siqueira
Microorganisms 2022, 10(8), 1670; https://doi.org/10.3390/microorganisms10081670 - 19 Aug 2022
Cited by 1 | Viewed by 1322
Abstract
This work focused on obtaining fermented oil cake (cotton or Jatropha) via macrofungi growth with potential characteristics for animal feed formulations, such as the presence of extracellular enzymes, bioactive (ergosterol and antioxidants), and detoxification of antinutritional compounds. The concentration of phorbol esters [...] Read more.
This work focused on obtaining fermented oil cake (cotton or Jatropha) via macrofungi growth with potential characteristics for animal feed formulations, such as the presence of extracellular enzymes, bioactive (ergosterol and antioxidants), and detoxification of antinutritional compounds. The concentration of phorbol esters was reduced by four macrofungi in Jatropha seed cake (JSC) to non-toxic levels. At least two macrofungi efficiently degraded free gossypol in cottonseed cake (CSC). Fermentation with Coriolopsis sp. INPA1646 and Tyromyces sp. INPA1696 resulted in increased ergosterol concentrations, antioxidant activity reduction, and high activity of laccases and proteases. Bromatological analysis indicated high crude protein concentrations, with partial solubilization by fungal proteases. Fermented products from Coriolopsis sp. and Tyromyces sp. in JSC or CSC can be considered important biological inputs for monogastric and polygastric animal feed. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions)
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24 pages, 2961 KiB  
Article
Dynamics of Starter and Non-Starter Lactic Acid Bacteria Populations in Long-Ripened Cheddar Cheese Using Propidium Monoazide (PMA) Treatment
by Zoha Barzideh, Myra Siddiqi, Hassan Mahmoud Mohamed and Gisèle LaPointe
Microorganisms 2022, 10(8), 1669; https://doi.org/10.3390/microorganisms10081669 - 19 Aug 2022
Cited by 8 | Viewed by 1809
Abstract
The microbial community of industrially produced Canadian Cheddar cheese was examined from curd to ripened cheese at 30–32 months using a combination of viable plate counts of SLAB (GM17) and NSLAB (MRSv), qPCR and 16S rRNA gene amplicon sequencing. Cell treatment with propidium [...] Read more.
The microbial community of industrially produced Canadian Cheddar cheese was examined from curd to ripened cheese at 30–32 months using a combination of viable plate counts of SLAB (GM17) and NSLAB (MRSv), qPCR and 16S rRNA gene amplicon sequencing. Cell treatment with propidium monoazide excluded DNA of permeable cells from amplification. The proportion of permeable cells of both Lactococcus spp. and Lacticaseibacillus spp. was highest at 3–6 months. While most remaining Lacticaseibacillus spp. cells were intact during later ripening stages, a consistent population of permeable Lactococcus spp. cells was maintained over the 32-month period. While Lactococcus sequence variants were significant biomarkers for viable cheese curd communities at 0–1 m, Lacticaseibacillus was identified as a distinctive biomarker for cheeses from 7 to 20 months. From 24 to 32 months, Lacticaseibacillus was replaced in significance by four genera (Pediococcus and Latilactobacillus at 24 m and at 30–32 m, Secundilactobacillus and Paucilactobacillus). These results underscore the importance of monitoring potential defects in cheeses aged over 24 months, which could be diagnosed early through microbial DNA profiling to minimize potential waste of product. Future perspectives include correlating volatile flavor compounds with microbial community composition as well as the investigation of intra-species diversity. Full article
(This article belongs to the Special Issue Microbial Ecology of Dairy Products: From Diversity to Functions)
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13 pages, 2007 KiB  
Article
Bacterial Prevalence in Skin, Urine, Diarrheal Stool, and Respiratory Samples from Dogs
by Dong-Chan Moon, Ji-Hyun Choi, Naila Boby, Hee-Young Kang, Su-Jeong Kim, Hyun-Ju Song, Ho-Sung Park, Min-Chan Gil, Soon-Seek Yoon and Suk-Kyung Lim
Microorganisms 2022, 10(8), 1668; https://doi.org/10.3390/microorganisms10081668 - 19 Aug 2022
Cited by 3 | Viewed by 1944
Abstract
The emergence of bacterial infections in companion animals is a growing concern as humans can also be infected through the transmission of pathogenic bacteria. Because there have been few studies conducted on companion animals, the extent and significance of prevalence in veterinary practices [...] Read more.
The emergence of bacterial infections in companion animals is a growing concern as humans can also be infected through the transmission of pathogenic bacteria. Because there have been few studies conducted on companion animals, the extent and significance of prevalence in veterinary practices remain unknown. This is the first nationwide surveillance report aimed at elucidating the prevalence pattern and associated infections of isolated bacteria from dogs in Korea. Bacterial isolates were collected from seven different laboratories participating in the Korean Veterinary Antimicrobial Resistance Monitoring System from 2018 to 2019. The samples were obtained from the diarrheal stool, skin/ear, urine, and respiratory samples of veterinary hospital-visited dogs. Isolation and identification of bacterial species was carried out using a bacterial culture approach and then confirmed with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF) and polymerase chain reaction (PCR). Out of 3135 isolates in dogs, 1085, 1761, 171, and 118 were extracted from diarrheal stool, skin/ear, urine, and respiratory samples, respectively. The overall prevalence of bacteria was higher among two age groups (1–5 and 6–10 years) with a 66.5 percent prevalence. This study showed that Escherichia coli was the most prevalent species among isolated bacterial species of diarrheal and urine origin, whereas Staphylococcus pseudintermedius was the most prevalent among skin and respiratory sample isolates. The data on the prevalence of bacteria for each dog specimen could provide basic information to estimate the extent of bacterial infection and antimicrobial resistance development and to guide veterinarians in therapeutic decisions in clinical practices throughout Korea. Full article
(This article belongs to the Section Public Health Microbiology)
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17 pages, 8517 KiB  
Article
A Comparison of Rhizospheric and Endophytic Bacteria in Early and Late-Maturing Pumpkin Varieties
by Siyu Chen, Renliu Qin, Da Yang, Wenjun Liu and Shangdong Yang
Microorganisms 2022, 10(8), 1667; https://doi.org/10.3390/microorganisms10081667 - 18 Aug 2022
Cited by 3 | Viewed by 2043
Abstract
To determine whether rhizospheric and endophytic bacteria contribute to the ripening of pumpkins, an analysis was conducted on rhizospheric and endophytic bacteria and soil fertility in the rhizospheres of early and late-maturing pumpkin varieties. The results showed higher nitrogen and abscisic acid content [...] Read more.
To determine whether rhizospheric and endophytic bacteria contribute to the ripening of pumpkins, an analysis was conducted on rhizospheric and endophytic bacteria and soil fertility in the rhizospheres of early and late-maturing pumpkin varieties. The results showed higher nitrogen and abscisic acid content and more gibberellin-producing bacteria in the rhizospheres or endophytes of the early maturing varieties. Greater soil fertility and more abundant rhizospheric and endophytic bacterial genera with a greater metabolic function might be important mechanisms for early ripening. Rhodococcus, Bacillus, and Arthrobacter can be considered the functional bacteria in promoting pumpkin maturation. On the other hand, Ralstonia could be the functional bacterium that delays ripening. Full article
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12 pages, 632 KiB  
Article
SARS-CoV-2 Vaccination Coverage and Factors Associated with Low Uptake in a Cohort of People Living with HIV
by Daniel Kwakye Nomah, Josep Maria Llibre, Yesika Díaz, Sergio Moreno, Jordi Aceiton, Andreu Bruguera, Maria Gutiérrez-Macià, Arkaitz Imaz, Paula Suanzes, Gemma Navarro, Amat Orti, Jose Maria Miro, Jordi Casabona, Juliana Reyes-Urueña and the PISCIS Study Group
Microorganisms 2022, 10(8), 1666; https://doi.org/10.3390/microorganisms10081666 - 18 Aug 2022
Cited by 6 | Viewed by 1534
Abstract
People living with HIV (PLWH) are prioritised for SARS-CoV-2 vaccination due to their vulnerability to severe COVID-19. Therefore, the epidemiological surveillance of vaccination coverage and the timely identification of suboptimally vaccinated PLWH is vital. We assessed SARS-CoV-2 vaccination coverage and factors associated with [...] Read more.
People living with HIV (PLWH) are prioritised for SARS-CoV-2 vaccination due to their vulnerability to severe COVID-19. Therefore, the epidemiological surveillance of vaccination coverage and the timely identification of suboptimally vaccinated PLWH is vital. We assessed SARS-CoV-2 vaccination coverage and factors associated with under-vaccination among PLWH in Catalonia, Spain. As of 11.12.2021, 9945/14942 PLWH (66.6%) had received ≥1 dose of a SARS-CoV-2 vaccine. Non-Spanish origin (adjusted odds ratio (aOR) 0.64, 95% CI 0.59–0.70), CD4 count of 200–349 cells/μL (aOR 0.74, 95% CI 0.64–0.86) or 350–499 cells/μL (aOR 0.79, 95% CI 0.70–0.88), detectable plasma HIV-RNA (aOR 0.61 95% CI 0.53–0.70), and previous SARS-CoV-2 diagnosis (aOR 0.58 95% CI 0.51–0.65) were associated with under-vaccination. SARS-CoV-2 diagnosis (437 [9.5%] vs. 323 [3.5%], p < 0.001), associated hospitalisations (10 [2.3%] vs. 0 [0%], p < 0.001), intensive care unit admissions (6 [1.4%] vs. 0 [0%], p < 0.001), and deaths (10 [2.3%] vs. 0 [0%], p < 0.001) were higher among unvaccinated PLWH. Vaccination coverage was lower among PLWH with a CD4 count >200 cells/μL, detectable plasma HIV-RNA, previous SARS-CoV-2 diagnosis, and migrants. SARS-CoV-2 diagnosis, associated hospitalisations, and deaths among PLWH were lower among the vaccinated compared with the unvaccinated. SARS-CoV-2 vaccination prioritisation has not completely reached vulnerable PLWH with poorer prognosis. This information can be used to inform public health strategies. Full article
(This article belongs to the Section Public Health Microbiology)
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3 pages, 186 KiB  
Correction
Correction: Ravin et al. Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov. Microorganisms 2022, 10, 1300
by Nikolai V. Ravin, Simona Rossetti, Alexey V. Beletsky, Vitaly V. Kadnikov, Tatyana S. Rudenko, Dmitry D. Smolyakov, Marina I. Moskvitina, Maria V. Gureeva, Andrey V. Mardanov and Margarita Yu. Grabovich
Microorganisms 2022, 10(8), 1665; https://doi.org/10.3390/microorganisms10081665 - 18 Aug 2022
Cited by 1 | Viewed by 929
Abstract
The authors wish to make the following corrections to this paper [...] Full article
(This article belongs to the Special Issue Genome Analysis of Microbial Communities in the Environment)
13 pages, 1942 KiB  
Review
Strategies for the Biodegradation of Polyfluorinated Compounds
by Lawrence P. Wackett
Microorganisms 2022, 10(8), 1664; https://doi.org/10.3390/microorganisms10081664 - 17 Aug 2022
Cited by 8 | Viewed by 3223
Abstract
Many cite the strength of C–F bonds for the poor microbial biodegradability of polyfluorinated organic compounds (PFCs). However, commercial PFCs almost invariably contain more functionality than fluorine. The additional functionality provides a weak entry point for reactions that activate C–F bonds and lead [...] Read more.
Many cite the strength of C–F bonds for the poor microbial biodegradability of polyfluorinated organic compounds (PFCs). However, commercial PFCs almost invariably contain more functionality than fluorine. The additional functionality provides a weak entry point for reactions that activate C–F bonds and lead to their eventual cleavage. This metabolic activation strategy is common in microbial biodegradation pathways and is observed with aromatic hydrocarbons, chlorinated compounds, phosphonates and many other compounds. Initial metabolic activation precedes critical bond breakage and assimilation of nutrients. A similar strategy with commercial PFCs proceeds via initial attack at the non-fluorinated functionalities: sulfonates, carboxylates, chlorines, phenyl rings, or phosphonates. Metabolic transformation of these non-fluorinated groups can activate the C–F bonds, allowing more facile cleavage than a direct attack on the C–F bonds. Given that virtually all compounds denoted as “PFAS” are not perfluorinated and are not alkanes, it is posited here that considering their individual chemical classes is more useful for both chemical and microbiological considerations of their fate. Full article
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16 pages, 3996 KiB  
Article
Spatio-Temporal Patterns of Ticks and Molecular Survey of Anaplasma marginale, with Notes on Their Phylogeny
by Shumaila Alam, Mehran Khan, Abdulaziz Alouffi, Mashal M. Almutairi, Shafi Ullah, Muhammad Numan, Nabila Islam, Zaibullah Khan, Ome Aiman, Sher Zaman Safi, Tetsuya Tanaka and Abid Ali
Microorganisms 2022, 10(8), 1663; https://doi.org/10.3390/microorganisms10081663 - 17 Aug 2022
Cited by 17 | Viewed by 2111
Abstract
Hard ticks (Ixodida: Ixodidae) are medically important ectoparasites that feed on all classes of terrestrial vertebrates. Recently, we molecularly characterized hard ticks and associated Anaplasma spp. in the northern and central regions of Khyber Pakhtunkhwa (KP), Pakistan; however, this knowledge was missing in [...] Read more.
Hard ticks (Ixodida: Ixodidae) are medically important ectoparasites that feed on all classes of terrestrial vertebrates. Recently, we molecularly characterized hard ticks and associated Anaplasma spp. in the northern and central regions of Khyber Pakhtunkhwa (KP), Pakistan; however, this knowledge was missing in the southern regions. This study aimed to investigate tick prevalence, host range, genetic diversity, and molecular survey of Anaplasma spp. in a wide range of tick species in two distinct physiographic regions of southern KP. A total of 1873 hard ticks were randomly collected from 443/837 hosts (cattle, Asian water buffaloes, horses, goats, sheep, dogs, and camels) in Lakki Marwat, Bannu, and Orakzai districts of KP. Overall, 12 tick species were morphologically identified, among which Hyalomma dromedarii was the most prevalent species (390/1873, 20.9%), followed by Hy. anatolicum (294, 15.7%), Rhipicephalus microplus (262, 14%), Hy. scupense (207, 11.1%), R. sanguineus (136, 7.3%), R. turanicus (121, 6.5%), Haemaphysalis cornupunctata (107, 5.7%), R. haemaphysaloides (110, 5.9%), Ha. montgomeryi (87, 4.6%), Hy. isaaci (58, 3.1%), Ha. bispinosa (54, 2.9%), and Ha. sulcata (47, 2.5%). The extracted DNA from a subset of each tick species was subjected to PCR to amplify cox1 or 16S rRNA sequences of ticks and 16S rRNA sequences of Anaplasma spp. The tick cox1 sequences showed 99–100% identities with the sequences of the same species, whereas 16S rRNA sequences of R. turanicus, Ha. montgomeryi and Ha. sulcata showed 97–100% identities with the corresponding species. The 16S rRNA sequence of Ha. cornupunctata showed 92% identity with the species from the same subgenus, such as Ha. punctata. The 16S rRNA sequence of Anaplasma spp. showed 100% identity with Anaplasma marginale. Moreover, 54 ticks were found positive for A. marginale with a total infection rate of 17.2%. The highest infection rate was recorded in Hy. dromedarii (31.1%) and the lowest in each R. haemaphysaloides and R. sanguineus (20%). All the cox1 or 16S rRNA sequences in phylogenetic trees clustered with the same species, except Ha. cornupunctata, which clustered with the Ha. (Aboimisalis) punctata. In this study, Ha. cornupunctata was reported for the first time at the molecular level. The genetic characterization of ixodid ticks and molecular detection of associated A. marginale will assist in the epidemiological surveillance of these parasites in the region. Full article
(This article belongs to the Special Issue Molecular Detection and Genotypic Analysis of Tick-Borne Pathogens)
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20 pages, 40809 KiB  
Article
Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes
by Yibi Chen, Sarah Shah, Katherine E. Dougan, Madeleine J. H. van Oppen, Debashish Bhattacharya and Cheong Xin Chan
Microorganisms 2022, 10(8), 1662; https://doi.org/10.3390/microorganisms10081662 - 17 Aug 2022
Cited by 9 | Viewed by 2899
Abstract
Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence [...] Read more.
Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35–36% have putatively originated via horizontal gene transfer (HGT), predominantly (19–23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10–11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates. Full article
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11 pages, 2198 KiB  
Review
The Genus Iodidimonas: From Its Discovery to Potential Applications
by Seigo Amachi and Takao Iino
Microorganisms 2022, 10(8), 1661; https://doi.org/10.3390/microorganisms10081661 - 17 Aug 2022
Cited by 3 | Viewed by 2004
Abstract
The genus Iodidimonas was recently proposed in the class Alphaproteobacteria. Iodidimonas strains are aerobic, mesophilic, neutrophilic, moderately halophilic, and chemo-organotrophic. They were first discovered in natural gas brine water containing a very high level of iodide (I). They exhibited a unique [...] Read more.
The genus Iodidimonas was recently proposed in the class Alphaproteobacteria. Iodidimonas strains are aerobic, mesophilic, neutrophilic, moderately halophilic, and chemo-organotrophic. They were first discovered in natural gas brine water containing a very high level of iodide (I). They exhibited a unique phenotypic feature of iodide oxidation to form molecular iodine (I2). Iodidimonas was also enriched and isolated from surface seawater supplemented with iodide, and it is clearer now that their common habitats are those enriched with iodide. In such environments, Iodidimonas species seem to attack microbial competitors with the toxic form I2 to occupy their ecological niche. The iodide-oxidizing enzyme (IOX) purified from the Iodidimonas sp. strain Q-1 exhibited high catalytic efficiency for iodide and consisted of at least two proteins IoxA and IoxC. IoxA is a putative multicopper oxidase with four conserved copper-binding regions but is phylogenetically distinct from other bacterial multicopper oxidases. The IOX/iodide system could be used as a novel enzyme-based antimicrobial system which can efficiently kill Bacillus spores. Furthermore, the IOX/iodide system can be applied to the decolorization of recalcitrant dyes, where iodide may function as a novel inorganic natural redox mediator. Full article
(This article belongs to the Special Issue Bacterial Evolution – Molecular Adaptation to Oxygen)
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11 pages, 2000 KiB  
Article
Molecular Evolution of the Pseudomonas aeruginosa DNA Gyrase gyrA Gene
by Mitsuru Sada, Hirokazu Kimura, Norika Nagasawa, Mao Akagawa, Kaori Okayama, Tatsuya Shirai, Soyoka Sunagawa, Ryusuke Kimura, Takeshi Saraya, Haruyuki Ishii, Daisuke Kurai, Takeshi Tsugawa, Atsuyoshi Nishina, Haruyoshi Tomita, Mitsuaki Okodo, Shinichiro Hirai, Akihide Ryo, Taisei Ishioka and Koichi Murakami
Microorganisms 2022, 10(8), 1660; https://doi.org/10.3390/microorganisms10081660 - 17 Aug 2022
Cited by 5 | Viewed by 1911
Abstract
DNA gyrase plays important roles in genome replication in various bacteria, including Pseudomonasaeruginosa. The gyrA gene encodes the gyrase subunit A protein (GyrA). Mutations in GyrA are associated with resistance to quinolone-based antibiotics. We performed a detailed molecular evolutionary analyses of [...] Read more.
DNA gyrase plays important roles in genome replication in various bacteria, including Pseudomonasaeruginosa. The gyrA gene encodes the gyrase subunit A protein (GyrA). Mutations in GyrA are associated with resistance to quinolone-based antibiotics. We performed a detailed molecular evolutionary analyses of the gyrA gene and associated resistance to the quinolone drug, ciprofloxacin, using bioinformatics techniques. We produced an evolutionary phylogenetic tree using the Bayesian Markov Chain Monte Carlo (MCMC) method. This tree indicated that a common ancestor of the gene was present over 760 years ago, and the offspring formed multiple clusters. Quinolone drug-resistance-associated amino-acid substitutions in GyrA, including T83I and D87N, emerged after the drug was used clinically. These substitutions appeared to be positive selection sites. The molecular affinity between ciprofloxacin and the GyrA protein containing T83I and/or D87N decreased significantly compared to that between the drug and GyrA protein, with no substitutions. The rate of evolution of the gene before quinolone drugs were first used in the clinic, in 1962, was significantly lower than that after the drug was used. These results suggest that the gyrA gene evolved to permit the bacterium to overcome quinolone treatment. Full article
(This article belongs to the Special Issue New Perspectives for the Control of Antimicrobial Resistance)
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18 pages, 2695 KiB  
Review
Anti-Toxoplasma gondii IgM Long Persistence: What Are the Underlying Mechanisms?
by José Antonio Vargas-Villavicencio, Irma Cañedo-Solares and Dolores Correa
Microorganisms 2022, 10(8), 1659; https://doi.org/10.3390/microorganisms10081659 - 17 Aug 2022
Cited by 5 | Viewed by 5018
Abstract
Diagnosis of Toxoplasma gondii acute infection was first attempted by detection of specific IgM antibodies, as for other infectious diseases. However, it was noted that this immunoglobulin declines slowly and may last for months or even years. Apart from the diagnostic problem imposed [...] Read more.
Diagnosis of Toxoplasma gondii acute infection was first attempted by detection of specific IgM antibodies, as for other infectious diseases. However, it was noted that this immunoglobulin declines slowly and may last for months or even years. Apart from the diagnostic problem imposed on clinical management, this phenomenon called our attention due to the underlying phenomena that may be causing it. We performed a systematic comparison of reports studying IgM antibody kinetics, and the data from the papers were used to construct comparative plots and other graph types. It became clear that this phenomenon is quite generalized, and it may also occur in animals. Moreover, this is not a technical issue, although some tests make more evident the prolonged IgM decay than others. We further investigated biological reasons for its occurrence, i.e., infection dynamics (micro-reactivation–encystment, reinfection and reactivation), parasite strain relevance, as well as host innate, natural B cell responses and Ig class-switch problems inflicted by the parasite. The outcomes of these inquiries are presented and discussed herein. Full article
(This article belongs to the Special Issue Parasitic Infection and Host Immunity)
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14 pages, 1540 KiB  
Article
Machine Learning Algorithms for Classification of MALDI-TOF MS Spectra from Phylogenetically Closely Related Species Brucella melitensis, Brucella abortus and Brucella suis
by Flavia Dematheis, Mathias C. Walter, Daniel Lang, Markus Antwerpen, Holger C. Scholz, Marie-Theres Pfalzgraf, Enrico Mantel, Christin Hinz, Roman Wölfel and Sabine Zange
Microorganisms 2022, 10(8), 1658; https://doi.org/10.3390/microorganisms10081658 - 17 Aug 2022
Cited by 7 | Viewed by 1972
Abstract
(1) Background: MALDI-TOF mass spectrometry (MS) is the gold standard for microbial fingerprinting, however, for phylogenetically closely related species, the resolution power drops down to the genus level. In this study, we analyzed MALDI-TOF spectra from 44 strains of B. melitensis, B. [...] Read more.
(1) Background: MALDI-TOF mass spectrometry (MS) is the gold standard for microbial fingerprinting, however, for phylogenetically closely related species, the resolution power drops down to the genus level. In this study, we analyzed MALDI-TOF spectra from 44 strains of B. melitensis, B. suis and B. abortus to identify the optimal classification method within popular supervised and unsupervised machine learning (ML) algorithms. (2) Methods: A consensus feature selection strategy was applied to pinpoint from among the 500 MS features those that yielded the best ML model and that may play a role in species differentiation. Unsupervised k-means and hierarchical agglomerative clustering were evaluated using the silhouette coefficient, while the supervised classifiers Random Forest, Support Vector Machine, Neural Network, and Multinomial Logistic Regression were explored in a fine-tuning manner using nested k-fold cross validation (CV) with a feature reduction step between the two CV loops. (3) Results: Sixteen differentially expressed peaks were identified and used to feed ML classifiers. Unsupervised and optimized supervised models displayed excellent predictive performances with 100% accuracy. The suitability of the consensus feature selection strategy for learning system accuracy was shown. (4) Conclusion: A meaningful ML approach is here introduced, to enhance Brucella spp. classification using MALDI-TOF MS data. Full article
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20 pages, 732 KiB  
Review
To Die or Not to Die—Regulated Cell Death and Survival in Cyanobacteria
by Natasha S. Barteneva, Ayagoz Meirkhanova, Dmitry Malashenkov and Ivan A. Vorobjev
Microorganisms 2022, 10(8), 1657; https://doi.org/10.3390/microorganisms10081657 - 17 Aug 2022
Cited by 3 | Viewed by 2450
Abstract
Regulated cell death (RCD) is central to the development, integrity, and functionality of multicellular organisms. In the last decade, evidence has accumulated that RCD is a universal phenomenon in all life domains. Cyanobacteria are of specific interest due to their importance in aquatic [...] Read more.
Regulated cell death (RCD) is central to the development, integrity, and functionality of multicellular organisms. In the last decade, evidence has accumulated that RCD is a universal phenomenon in all life domains. Cyanobacteria are of specific interest due to their importance in aquatic and terrestrial habitats and their role as primary producers in global nutrient cycling. Current knowledge on cyanobacterial RCD is based mainly on biochemical and morphological observations, often by methods directly transferred from vertebrate research and with limited understanding of the molecular genetic basis. However, the metabolism of different cyanobacteria groups relies on photosynthesis and nitrogen fixation, whereas mitochondria are the central executioner of cell death in vertebrates. Moreover, cyanobacteria chosen as biological models in RCD studies are mainly colonial or filamentous multicellular organisms. On the other hand, unicellular cyanobacteria have regulated programs of cellular survival (RCS) such as chlorosis and post-chlorosis resuscitation. The co-existence of different genetically regulated programs in cyanobacterial populations may have been a top engine in life diversification. Development of cyanobacteria-specific methods for identification and characterization of RCD and wider use of single-cell analysis combined with intelligent image-based cell sorting and metagenomics would shed more light on the underlying molecular mechanisms and help us to address the complex colonial interactions during these events. In this review, we focus on the functional implications of RCD in cyanobacterial communities. Full article
(This article belongs to the Special Issue Integrative Phylogeny, Physiology and Ecology of Cyanobacteria)
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